Add downloadable cells dataset via scverse-misc

.github/workflows/test.yaml

@@ -19,11 +19,11 @@ jobs:
             fail-fast: false
             matrix:
                 include:
-                    - {os: windows-latest, python: "3.11", dask-version: "2026.3.0", name: "min dask"}
+                    - {os: windows-latest, python: "3.12", dask-version: "2026.3.0", name: "min dask"}
                     - {os: windows-latest, python: "3.14", dask-version: "latest"}
-                    - {os: ubuntu-latest, python: "3.11", dask-version: "latest"}
+                    - {os: ubuntu-latest, python: "3.12", dask-version: "latest"}
                     - {os: ubuntu-latest, python: "3.14", dask-version: "latest"}
-                    - {os: macos-latest, python: "3.11", dask-version: "latest"}
+                    - {os: macos-latest, python: "3.12", dask-version: "latest"}
                     - {os: macos-latest, python: "3.14", prerelease: "allow", name: "prerelease"}
         env:
             OS: ${{ matrix.os }}
@@ -41,7 +41,7 @@ jobs:
             - name: Install dependencies
               run: |
                   if [[ "${PRERELEASE}" == "allow" ]]; then
-                    sed -i '' 's/requires-python.*//' pyproject.toml # otherwise uv complains that anndata requires python>=3.12 and we only do >=3.11 😱
+                    sed -i '' 's/requires-python.*//' pyproject.toml # drop the cap so uv can resolve prerelease deps
                     uv add git+https://github.com/scverse/anndata.git
                     uv add pandas>=3.dev0
                   fi

docs/api/datasets.md

@@ -7,5 +7,6 @@ Convenience small datasets
 
 .. autofunction:: blobs
 .. autofunction:: blobs_annotating_element
+.. autofunction:: cells
 .. autofunction:: raccoon
 ```

pyproject.toml

@@ -15,7 +15,7 @@ maintainers = [
 urls.Documentation = "https://spatialdata.scverse.org/en/latest"
 urls.Source = "https://github.com/scverse/spatialdata.git"
 urls.Home-page = "https://github.com/scverse/spatialdata.git"
-requires-python = ">=3.11"
+requires-python = ">=3.12"
 dynamic= [
   "version" # allow version to be set by git tags
 ]
@@ -45,6 +45,7 @@ dependencies = [
     "spatial_image>=1.2.3",
     "scikit-image",
     "scipy!=1.17.0",
+    "scverse-misc[datasets]>=0.0.10",
     "typing_extensions>=4.8.0",
     "universal_pathlib>=0.2.6",
     "xarray>=2024.10.0",
@@ -145,7 +146,7 @@ exclude = [
 
 ]
 line-length = 120
-target-version = "py311"
+target-version = "py312"
 
 [tool.ruff.lint]
 ignore = [

src/spatialdata/datasets.py

@@ -31,7 +31,7 @@
 )
 from spatialdata.transformations import Identity
 
-__all__ = ["blobs", "raccoon"]
+__all__ = ["blobs", "cells", "raccoon"]
 
 
 def blobs(
@@ -79,6 +79,37 @@ def raccoon() -> SpatialData:
     return RaccoonDataset().raccoon()
 
 
+def cells(path: str | None = None) -> SpatialData:
+    """
+    Cells dataset.
+
+    Download the ``cells`` example dataset and load it as a :class:`~spatialdata.SpatialData`
+    object. The download is hash-verified and cached, so repeated calls reuse the local copy
+    instead of downloading again.
+
+    Parameters
+    ----------
+    path
+        Directory in which to cache the downloaded data. If `None`, the default OS cache
+        location is used (:func:`pooch.os_cache` for ``"spatialdata"``).
+
+    Returns
+    -------
+    SpatialData object with the cells dataset.
+    """
+    import importlib.resources
+    from pathlib import Path
+
+    import pooch
+    from scverse_misc.datasets import fetch, parse_registry
+
+    cache_dir = Path(path) if path is not None else Path(pooch.os_cache("spatialdata"))
+    registry = importlib.resources.files("spatialdata").joinpath("datasets.yaml")
+    with importlib.resources.as_file(registry) as registry_path:
+        base_url, datasets = parse_registry(registry_path)
+    return fetch(datasets["cells"], cache_dir, base_url=base_url)
+
+
 class RaccoonDataset:
     """Raccoon dataset."""
 

src/spatialdata/datasets.yaml

@@ -0,0 +1,15 @@
+# Registry of downloadable example datasets for ``spatialdata.datasets``.
+#
+# Parsed by ``scverse_misc.datasets.parse_registry`` and fetched (downloaded,
+# hash-verified, cached and loaded) via ``scverse_misc.datasets.fetch``.
+#
+#   type: spatialdata  ->  a .zip that extracts to a single .zarr store
+base_url: https://exampledata.scverse.org/spatialdata/
+datasets:
+    cells:
+        type: spatialdata
+        doc_header: Cells dataset as a SpatialData object.
+        files:
+            - name: cells.zip
+              s3_key: cells.zip
+              sha256: dc9613cb9e16fd2cd8d83f3a9586eeda4af5ba8ba366f1066efb51305820c5fb

tests/datasets/test_datasets.py

@@ -1,6 +1,11 @@
 from __future__ import annotations
 
-from spatialdata.datasets import blobs, raccoon
+import importlib.resources
+
+import pytest
+
+from spatialdata import SpatialData
+from spatialdata.datasets import blobs, cells, raccoon
 
 
 def test_datasets() -> None:
@@ -26,3 +31,26 @@ def test_datasets() -> None:
     assert sdata_raccoon.images["raccoon"].shape == (3, 768, 1024)
     assert sdata_raccoon.labels["segmentation"].shape == (768, 1024)
     _ = str(sdata_raccoon)
+
+
+def test_cells_registry() -> None:
+    # Network-free: the shipped registry parses and exposes the cells dataset.
+    from scverse_misc.datasets import parse_registry
+
+    registry = importlib.resources.files("spatialdata").joinpath("datasets.yaml")
+    with importlib.resources.as_file(registry) as registry_path:
+        base_url, datasets = parse_registry(registry_path)
+
+    assert base_url == "https://exampledata.scverse.org/spatialdata/"
+    entry = datasets["cells"]
+    assert entry.type == "spatialdata"
+    file = entry.file(name="cells.zip")
+    assert file.sha256 == "dc9613cb9e16fd2cd8d83f3a9586eeda4af5ba8ba366f1066efb51305820c5fb"
+    assert file.resolve_url(base_url) == "https://exampledata.scverse.org/spatialdata/cells.zip"
+
+
+@pytest.mark.slow
+def test_cells_download(tmp_path) -> None:
+    # Downloads ~3 MB from the scverse example data bucket; opt out with `-m "not slow"`.
+    sdata = cells(path=str(tmp_path))
+    assert isinstance(sdata, SpatialData)